def closest(self, atom_type, reference, n=1, exclude=False, only=False):
'''
If n=1: return the number in the xyz matrix of the atom of atom_type
which is the closest to a reference atom in a geometry.
If n>1, return a list of the n closest atoms of atom_type, which are
closest to the reference atom.
Arguments:
atom_type: atom number or symbol of the atoms whose number
in the xyz matrix
must be returned
reference: number of the reference atom in the xyz matrix
n: number of atoms to return
exclude: exclude these atoms
only: limit search to these atoms
'''
# If search is not restricted, look for any atom.
if not only:
only = range(self.size)
atom_type = utils.anum(atom_type)
distances = self.distance_matrix[reference]
out = [
np.where(distances == d)[0][0] for d in sorted(distances)
if self.numbers[np.where(distances == d)[0][0]] == atom_type
and np.where(distances == d)[0][0] != reference and np.where(
distances == d)[0][0] in only
]
if exclude:
out = [o for o in out if o not in exclude]
if n > 1:
return out[:n]
elif n == 1:
return out[0]
def closest(self, atom_type, reference, n=1, exclude=False, only=False):
'''
If n=1: return the number in the xyz matrix of the atom of atom_type
which is the closest to a reference atom in a geometry.
If n>1, return a list of the n closest atoms of atom_type, which are
closest to the reference atom.
Arguments:
atom_type: atom number or symbol of the atoms whose number
in the xyz matrix
must be returned
reference: number of the reference atom in the xyz matrix
n: number of atoms to return
exclude: exclude these atoms
only: limit search to these atoms
'''
# If search is not restricted, look for any atom.
if not only:
only = range(self.size)
atom_type = utils.anum(atom_type)
distances = self.distance_matrix[reference]
out = [np.where(distances == d)[0][0] for d in sorted(distances)
if self.numbers[np.where(distances == d)[0][0]] == atom_type
and np.where(distances == d)[0][0] != reference
and np.where(distances == d)[0][0] in only]
if exclude:
out = [o for o in out if o not in exclude]
if n > 1:
return out[:n]
elif n == 1:
return out[0]
def __getitem__(self, i):
'''both Stoichio['C'] and Stoichio[6] will yield the number
of carbon atoms'''
try:
return self._array[utils.anum(i)]
# What happens if the number of Hf atoms is requested,
# but only atoms up to Cl are included?
except IndexError:
return 0
def __getitem__(self, i):
'''both Stoichio['C'] and Stoichio[6] will yield the number
of carbon atoms'''
try:
return self._array[utils.anum(i)]
# What happens if the number of Hf atoms is requested,
# but only atoms up to Cl are included?
except IndexError:
return 0
def from_string(cls, string, ignore_header=False):
''' handles both symbols and numbers,
take three last cols and first col'''
atoms = []
coordinates = []
for i, l in enumerate(string.strip().split('\n')):
if ignore_header and i < 2:
continue
split = l.split()
atoms.append(utils.anum(split[0]))
coordinates.append(
np.array(map(float, split[-3:])) * units.angstrom)
return cls.from_Molecule(mol.Molecule(atoms, coordinates))
def from_string(cls, string, ignore_header=False):
''' handles both symbols and numbers,
take three last cols and first col'''
atoms = []
coordinates = []
for i, l in enumerate(string.strip().split('\n')):
if ignore_header and i < 2:
continue
split = l.split()
atoms.append(utils.anum(split[0]))
coordinates.append(np.array(map(float, split[-3:]))
* units.angstrom)
return cls.from_Molecule(mol.Molecule(atoms, coordinates))
def _atomstr(self, z):
'''print things like 'C6' based on the atom number (z) or even
the atom symbol'''
try:
n = self._array[utils.anum(z)]
except:
n = 0
if n:
if n > 1:
return '%s%i' % (utils.asym(z).upper(), n)
elif n == 1:
return '%s' % utils.asym(z).upper()
else:
return ''
def _atomstr(self, z):
'''print things like 'C6' based on the atom number (z) or even
the atom symbol'''
try:
n = self._array[utils.anum(z)]
except:
n = 0
if n:
if n > 1:
return '%s%i' % (utils.asym(z).upper(), n)
elif n == 1:
return '%s' % utils.asym(z).upper()
else:
return ''
def atoms(self, at):
'''return the indices of the atoms with the given atom number or symbol'''
atom_type = utils.anum(at)
return numpy.where(self.numbers == atom_type)[0]
def atoms(self, at):
'''return the indices of the atoms with the given atom number or symbol'''
atom_type = utils.anum(at)
return numpy.where(self.numbers == atom_type)[0]
def _convert(atom):
try:
return mg.HasAtomNumber(utils.anum(atom))
except:
return atom